diff --git a/lib/galaxy/config/sample/tool_conf.xml.sample b/lib/galaxy/config/sample/tool_conf.xml.sample index 841f054b93d0..7ddcec93af91 100644 --- a/lib/galaxy/config/sample/tool_conf.xml.sample +++ b/lib/galaxy/config/sample/tool_conf.xml.sample @@ -140,6 +140,7 @@ + diff --git a/tools/interactive/interactivetool_jupyter_notebook_1.0.0.xml b/tools/interactive/interactivetool_jupyter_notebook_1.0.0.xml index 5b5e91e16144..870ecd19fd28 100644 --- a/tools/interactive/interactivetool_jupyter_notebook_1.0.0.xml +++ b/tools/interactive/interactivetool_jupyter_notebook_1.0.0.xml @@ -2,6 +2,9 @@ quay.io/bgruening/docker-jupyter-notebook:2021-03-05 + + + 8888 diff --git a/tools/interactive/interactivetool_jupyter_notebook_1.0.1.xml b/tools/interactive/interactivetool_jupyter_notebook_1.0.1.xml new file mode 100644 index 000000000000..8c249e289af2 --- /dev/null +++ b/tools/interactive/interactivetool_jupyter_notebook_1.0.1.xml @@ -0,0 +1,271 @@ + + + quay.io/bgruening/docker-jupyter-notebook:24.07 + + + + + + + 8888 + ipython/lab + + + + $__history_id__ + $__galaxy_url__ + 8080 + $__galaxy_url__ + + jupytool + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Welcome to the **JupyTool**! Here you can create, run, and share custom Galaxy tools based upon Jupyter Notebooks. + + The Jupyter Notebook is an open-source web application that allows you to create and share documents that contain live code, equations, + visualizations and narrative text. Uses include: data cleaning and transformation, numerical simulation, statistical modeling, data visualization, + machine learning, and much more. + + Galaxy offers you to use Jupyter Notebooks directly in Galaxy accessing and interacting with Galaxy datasets as you like. A very common use-case is to + do the heavy lifting and data reduction steps in Galaxy and the plotting and more `interactive` part on smaller datasets in Jupyter. + + You can start with a new Jupyter notebook from scratch or load an already existing one, e.g. from your colleague and execute it on your dataset. + You can specify any number of user-defined inputs using the repeat input, providing `name` value, selecting the type of input, and then providing values. + + You can make the JupyTool reusable in a workflow, by allowing the user to specify input values for the defined input blocks. + Inputs can be accessed by `name` from the automatically provided `GALAXY_INPUTS` dictionary. + Outputs can be written automatically to the user's history by writing to the `outputs` directory for one individual file or to the `outputs/collection` directory for multiple files. + Using collection tools, you can parse out the individual elements from the collection, as needed. + + For backwards compatibility, you can import data into the notebook via a predefined `get()` function and write results back to Galaxy with a `put()` function. + +